North American monarch butterflies (Danaus plexippus) migrate annually between the USA/Canada and wintering grounds in Mexico and southern California. In contrast, monarchs in South and Central America do not migrate. To explore the genetic basis of this behavioral variation, we sequenced portions of genes involved in the production of cellular energy and compared these sequences between migratory (Boston Harbor Islands) and non-migratory (Ecuador) populations. Our results demonstrate that there is pronounced genetic differentiation between monarchs from North and South America. This pattern is consistent with the involvement of these genes in generating a trait, like migratory behavior, which differs between the two populations. As a follow-up to these experiments, we are sequencing portions of additional genes to see if the observed differences represent a genome-wide pattern or if they are restricted to genes involved in energy production and flight performance.